JAL-3390 refactoring tidy of colourBySequence call stack

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index f0ae6dc..5243b40 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -486,8 +486,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param commands
    */
   @Override
-  protected void colourBySequence(final String[] commands)
+  protected void colourBySequence(AlignmentViewPanel viewPanel)
   {
+    Map<Object, AtomSpecModel> map = StructureCommands.buildColoursMap(this,
+            viewPanel);
+
+    String[] commands = JmolCommands.getColourBySequenceCommand(map);
+
     if (colourby != null)
     {
       colourby.interrupt();
@@ -508,20 +513,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * @param files
-   * @param viewPanel
-   * @return
-   */
-  @Override
-  protected String[] getColourBySequenceCommands(
-          String[] files, AlignmentViewPanel viewPanel)
-  {
-    Map<Object, AtomSpecModel> map = StructureCommands.buildColoursMap(this, viewPanel);
-
-    return JmolCommands.getColourBySequenceCommand(map);
-  }
-
-  /**
    * @param command
    */
   protected void executeWhenReady(String command)

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index dd0a75e..2846f32 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -647,13 +647,19 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           String progressMsg);
 
   /**
-   * Sends a set of colour commands to the structure viewer
+   * Constructs a set of colour commands and sends them to the structure viewer
    * 
-   * @param commands
+   * @param viewPanel
    */
   @Override
-  protected void colourBySequence(String[] commands)
+  protected void colourBySequence(AlignmentViewPanel viewPanel)
   {
+    Map<Object, AtomSpecModel> colourMap = StructureCommands
+            .buildColoursMap(this, viewPanel);
+
+    String[] commands = ChimeraCommands
+            .getColourBySequenceCommand(colourMap, this);
+
     for (String command : commands)
     {
       sendAsynchronousCommand(command, COLOURING_CHIMERA);
@@ -661,23 +667,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Computes and returns a set of commands to colour residues in Chimera the same
-   * as mapped residues in the alignment
-   * 
-   * @param files
-   * @param viewPanel
-   * @return
-   */
-  @Override
-  protected String[] getColourBySequenceCommands(
-          String[] files, AlignmentViewPanel viewPanel)
-  {
-    Map<Object, AtomSpecModel> colourMap = StructureCommands.buildColoursMap(this, viewPanel);
-
-    return ChimeraCommands.getColourBySequenceCommand(colourMap, this);
-  }
-
-  /**
    * @param command
    */
   protected void executeWhenReady(String command)
@@ -1022,6 +1011,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /**
    * Send a 'focus' command to Chimera to recentre the visible display
    */
+  @Override
   public void focusView()
   {
     sendChimeraCommand("focus", false);

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index af5fd0a..448ed24 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -783,9 +783,6 @@ public abstract class AAStructureBindingModel
 
   public abstract void setBackgroundColour(Color col);
 
-  protected abstract String[] getColourBySequenceCommands(
-          String[] files, AlignmentViewPanel avp);
-
   /**
    * returns the current sequenceRenderer that should be used to colour the
    * structures
@@ -797,8 +794,14 @@ public abstract class AAStructureBindingModel
   public abstract SequenceRenderer getSequenceRenderer(
           AlignmentViewPanel alignment);
 
-  protected abstract void colourBySequence(
-          String[] colourBySequenceCommands);
+  /**
+   * Recolours mapped residues in the structure viewer to match colours in the
+   * given alignment panel. Colours should also be applied to any hidden mapped
+   * residues (so that they are shown correctly if these get unhidden).
+   * 
+   * @param viewPanel
+   */
+  protected abstract void colourBySequence(AlignmentViewPanel viewPanel);
 
   public abstract void colourByChain();
 
@@ -834,11 +837,8 @@ public abstract class AAStructureBindingModel
     {
       return;
     }
-    String[] files = getStructureFiles();
 
-    String[] colourBySequenceCommands = getColourBySequenceCommands(
-            files, alignmentv);
-    colourBySequence(colourBySequenceCommands);
+    colourBySequence(alignmentv);
   }
 
   public boolean hasFileLoadingError()

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index 45e66ce..35fd179 100644 (file)
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -91,13 +91,6 @@ public class JmolCommandsTest
     }
 
     @Override
-    protected String[] getColourBySequenceCommands(String[] files,
-            AlignmentViewPanel avp)
-    {
-      return null;
-    }
-
-    @Override
     public jalview.api.SequenceRenderer getSequenceRenderer(
             AlignmentViewPanel alignment)
     {
@@ -105,7 +98,7 @@ public class JmolCommandsTest
     }
 
     @Override
-    protected void colourBySequence(String[] colourBySequenceCommands)
+    protected void colourBySequence(AlignmentViewPanel avp)
     {
     }
 

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index fb8626c..d5229c2 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -90,13 +90,6 @@ public class ChimeraCommandsTest
     }
 
     @Override
-    protected String[] getColourBySequenceCommands(String[] files,
-            AlignmentViewPanel avp)
-    {
-      return null;
-    }
-
-    @Override
     public jalview.api.SequenceRenderer getSequenceRenderer(
             AlignmentViewPanel alignment)
     {
@@ -104,7 +97,7 @@ public class ChimeraCommandsTest
     }
 
     @Override
-    protected void colourBySequence(String[] colourBySequenceCommands)
+    protected void colourBySequence(AlignmentViewPanel avp)
     {
     }
 

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 3992746..0bb1daf 100644 (file)
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -138,21 +138,16 @@ public class AAStructureBindingModelTest
       @Override
       public void updateColours(Object source)
       {
-        // TODO Auto-generated method stub
-        
       }
       
       @Override
       public void releaseReferences(Object svl)
       {
-        // TODO Auto-generated method stub
-        
       }
       
       @Override
       public String[] getStructureFiles()
       {
-        // TODO Auto-generated method stub
         return null;
       }
       
@@ -160,72 +155,49 @@ public class AAStructureBindingModelTest
       public String superposeStructures(AlignmentI[] alignments,
               int[] structureIndices, HiddenColumns[] hiddenCols)
       {
-        // TODO Auto-generated method stub
         return null;
       }
       
       @Override
       public void setJalviewColourScheme(ColourSchemeI cs)
       {
-        // TODO Auto-generated method stub
-        
       }
       
       @Override
       public void setBackgroundColour(Color col)
       {
-        // TODO Auto-generated method stub
-        
       }
       
       @Override
       public void highlightAtoms(List<AtomSpec> atoms)
       {
-        // TODO Auto-generated method stub
-        
       }
       
       @Override
       public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
       {
-        // TODO Auto-generated method stub
         return null;
       }
       
       @Override
       public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
       {
-        // TODO Auto-generated method stub
         return null;
       }
       
       @Override
-      protected String[] getColourBySequenceCommands(String[] files,
-              AlignmentViewPanel avp)
+      protected void colourBySequence(AlignmentViewPanel avp)
       {
-        // TODO Auto-generated method stub
-        return null;
-      }
-      
-      @Override
-      protected void colourBySequence(String[] colourBySequenceCommands)
-      {
-        // TODO Auto-generated method stub
-        
       }
       
       @Override
       public void colourByCharge()
       {
-        // TODO Auto-generated method stub
-        
       }
       
       @Override
       public void colourByChain()
       {
-        // TODO Auto-generated method stub
-        
       }
     };
     String[][] chains = binder.getChains();
@@ -313,13 +285,6 @@ public class AAStructureBindingModelTest
       }
 
       @Override
-      protected String[] getColourBySequenceCommands(
-              String[] files, AlignmentViewPanel avp)
-      {
-        return null;
-      }
-
-      @Override
       public SequenceRenderer getSequenceRenderer(
               AlignmentViewPanel alignment)
       {
@@ -327,7 +292,7 @@ public class AAStructureBindingModelTest
       }
 
       @Override
-      protected void colourBySequence(String[] colourBySequenceCommands)
+      protected void colourBySequence(AlignmentViewPanel avp)
       {
       }